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James Sacco
Laboratory for Genomics Research, Department of Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
Self-motivated computational biologist with six years of both academic and industry experience in: functional genomics (CRISPR-based screens), population genetics, and pipeline automation.
An analytical thinker and quick learner, with broad understanding of statistical and machine learning methods. Published author of research studies in the integration of genotype and phenotype data to model disease prevalence, and sub-types. Pre-clinical research experience in Mendelian disorders and immuno-oncology, specifically cancer immunotherapy. Advocate for diversity and inclusion of under-represented minorities in science.
Selected Experience
Bioinformatics Programmer III
Laboratory for Genomics Research & Department Biochemistry & Biophysics, University of California, San Francisco
San Francisco, CA
Present - 2022
● Led investigation of computational rules for CRISPRi guide design using open-source machine learning algorithms.
● Optimized of genome-wide CRISPRi/a transcriptional regulation in cancer cell lines, using epigenomic and genomic data analysis.
● Computational lead on CRISPR screen focused on lysosomal storage and mitochondrial dysfunction in Niemann-Pick Type C Disease.
● Integrated single-cell epigenetic and transcriptomic data to identify gene regulatory networks driving cell differentiation.
● Mentored junior programmers joining computational biology team.
Bioinformatics Scientist
ASC Therapeutics (Contract)
Milpitas, CA
2022 - 2021
● Quantifed and characterized CRISPR gene modifications, with both custom and open-source tools for genomic data analysis.
● Queried, retrieved, and integrated data from public genomics databases, to enhance on-target gene editing with sequence alignment protocols.
● Examined concordance and sensitivity of five computational CRISPR off-target detection methods.
● Streamlined high-performance analyses for bench scientists via custom data pipelines and user interfaces.
Biomarker Data Analyst II
Genentech (Contract)
South San Francisco, CA
2020 - 2019
● Established department-first machine learning pipeline to study effects of biomarker operations on quality of cancer immunotherapy assays.
● Upgraded data operations for six data streams, including flow cytometry, biomarker operations, and oncology data warehouses.
● Monitored and solved sample data quality issues for two cancer immunotherapy trial arms.
Data Curator
Genentech (Contract)
South San Francisco, CA
2019 - 2018
PROGRAMMING SKILLS
Python ★★★★★
R ★★★★★
Linux ★★★★★
Git ★★★★★
Markdown★★★★★
SQL ★★★☆☆
C++ ★★★☆☆
MATLAB ★★★☆☆
● Collaborated with AI engineers to create an ETL pipeline for multi-modal survival prediction and patient stratification, by using Python ML and R to integrate gene panel and RNA-Seq data.
● Designed ETL data pipeline for integration of real-world EHRs into deep learning module, using Python, SQL, and Apache Spark.
● Organized and managed close coordination of Artificial Intelligence, data management, and DevOps functions, to bring clinical machine learning from prototype to production.
Data Curator, Bioinformatics Analyst
BioMarin Pharmaceutical (Contract)
San Rafael, CA
2018 - 2017
● Established an integrated genetic and curated literature workflow to predict incidence and prevalence rates of over sixty rare, genetic disorders, with statistical and data visualization R packages (ggplot2) and MATLAB.
● Upgraded and tested RNA-Seq data pipeline (STAR2, SAMtools, Bioconductor) to discern disease contribution of rare variants to neural disease.
● Spearheaded development of three relational databases derived from Hail population genomics platform, in collaboration with software engineer.
● Co-authored manuscript submitted to peer-reviewed publication, on prediction of disease severity in metachromatic leukodystrophy.
● Developed allele-specific association models and GWAS analysis software for two later published manuscripts.
Research Associate
Pearse Lab: The Miami Project to Cure Paralysis, The Miller School of Medicine, University of Miami
Miami, FL
2017 - 2016
● Mentored research associates in developing bioinformatic skills, specifically in multiple sequence alignment and standard molecular biological protocols (restriction enzyme digestion, gel electrophoresis, spectrophotometry).
● Identified over forty putative conserved vertebrate phosphodiesterase proteins, by using multiple sequence alignment and genomic evidence.
Education
Rowan University, Graduate School of Biomedical Sciences
Master of Biomedical Science (Distinction)
Stratford, NJ
N/A
“Hippocampal long-term potentiation in neurodegenerative disorders”
I have participated in bioinformatics and software workshops and Meetup.com groups, in both Seattle, WA and San Francisco, CA, including:
SF/Bay AI Developers Group
San Jose Data Science and AI/ML Meetup
Hacker Dojo
Seattle Sequencing
LANGUAGES
English: Native
Spanish: Native
Dutch: Limited Working Proficiency
Related coursework:
● Biochemistry
● Molecular Biology
● Cell Biology
● Microbiology
● Pharmacology
Florida International University, The Honors College
BSc, Biological Sciences
Miami, FL
Professional Development
Publications
Regulating Axonal Responses to Injury: The Intersection between Signaling Pathways Involved in Axon Myelination and The Inhibition of Axon Regeneration.
Frontiers in Molecular Neuroscience. 2016 Jun 8;9:33.
N/A
2016
Rao S.N., Pearse D.D. Manuscript Editor
Conference Papers
Prediction of disease severity in metachromatic leukodystrophy using measures of protein activity and a novel phenotype matrix.
American Society of Human Genetics Virtual Meeting. [Poster] [Forthcoming in Genome Biology]
Online
2020
Trinidad M., Hong X., Sacco J., Nguyen H.P., Clark W.T., Froelich S., LeBowitz J.H., Gelb M.H.
Association of HGMD and gnomAD variants of unknown significance with prediction of disease incidence and prevalence.
BioMarin Internal Research and Development Asilomar Conference. [Poster]
Pacific Grove, CA
2018
Avid supporter of the San Francisco Symphony and San Francisco Conservatory of Music
Ultimate frisbee at Big Gay Frisbee. San Francisco, CA. 2018 – Present.
Salsa dance at In Lak’ech Dance Academy. Oakland, CA. 2019.
Rugby at Seattle Quake RFC. Seattle, WA. 2016 – 2017.
Sacco J., Clark W.T., Yu K., Wu K., LeBowitz J.H.
Research Projects
Characterization of glycan substrates accumulating in GM1 gangliosidosis
Molecular Genetics and Metabolism Reports. 2019. 21, p.100524.
N/A
2019
Lawrence R., et al.
Phosphodiesterase Inhibitors as a Therapeutic Approach to Neuroprotection and Repair
International Journal of Molecular Sciences. 2017. 18(4): 696.
N/A
2017
Knott E.P., et al.
Oral Communications
Data Visualization of RNA-Seq Differential Expression Analysis with DESeq2
Doudna Lab: Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley
Berkeley, CA
2022
Topics: Introduction to RNA-Seq, Standard Workflows with DESeq2, Reference-Based Assembly, Exploratory Data Analysis, Statistical Analysis, Data Visualization, Gene Set Enrichment, Variant Annotation
● Presented publication-quality RNA-Seq data summaries and representations to post-doctoral associates
Teaching
Peer-Led Team Learning
Florida International University
Miami, FL
2009
General Biology II facilitator for two concurrent PLTL courses
Disclaimer
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Last update: 2023-02-14.The most recent version of this resume is available here.